Revealing the Structure of an Accretion Disk Through Energy Dependent X-ray Microlensing

We present results from monitoring observations of the gravitationally lensed quasar RX J1131-1231 performed with the Chandra X-ray Observatory. The X-ray observations were planned with relatively long exposures that allowed a search for energy-dependent microlensing in the soft (0.2-2 keV) and hard (2-10 keV) light curves of the images of RX J1131-1231. We detect significant microlensing in the X-ray light-curves of images A and D, and energy-dependent microlensing of image D. The magnification of the soft band appears to be larger than that in the hard band by a factor of ~ 1.3 when image D becomes more magnified. This can be explained by the difference between a compact, softer-spectrum corona that is producing a more extended, harder spectrum reflection component off the disk. This is supported by the evolution of the fluorescent iron line in image D over three consecutive time-averaged phases of the light curve. In the first period, a Fe line at E = 6.36(-0.16,+0.13) keV is detected (at > 99% confidence). In the second period, two Fe lines are detected, one at E = 5.47(-0.08,+0.06) keV (detected at > 99% confidence) and another at E = 6.02(-0.07,+0.09) keV (marginally detected at > 90% confidence), and in the third period, a broadened Fe line at 6.42(-0.15,+0.19) keV is detected (at > 99% confidence). This evolution of the Fe line profile during the microlensing event is consistent with the line distortion expected when a caustic passes over the inner disk where the shape of the fluorescent Fe line is distorted by General Relativistic and Doppler effects.Comment: 20 pages, includes 10 figures, submitted to Ap

X-Ray and Optical Flux Anomalies in the Quadruply Lensed QSO 1RXS J1131-1231

Optical and X-ray observations of the quadruply imaged quasar 1RXS J1131-1231 show flux ratio anomalies among the images factors of ~2 in the optical and \~3-9 in X-rays. Temporal variability of the quasar seems an unlikely explanation for the discrepancies between the X-ray and optical flux ratio anomalies. The negative parity of the most affected image and the decreasing trend of the anomalies with wavelength suggest microlensing as a possible explanation; this would imply that the source of optical radiation in RXS J1131 is ~10^4 R_g in size for a black hole mass of ~10^8 M_sun. We also present evidence for different X-ray spectral hardness ratios among the four images.Comment: 5 pages, 1 color figure, replaced with version accepted to Ap

A Robust Determination of the size of quasar accretion disks using gravitational microlensing

Using microlensing measurements from a sample of 27 image-pairs of 19 lensed quasars we determine a maximum likelihood estimate for the accretion disk size of an {{\em}average} quasar of $r_s=4.0^{+2.4}_{-3.1}$ light days at rest frame $=1736$\AA\ for microlenses with a mean mass of $=0.3M_\odot$. This value, in good agreement with previous results from smaller samples, is roughly a factor of 5 greater than the predictions of the standard thin disk model. The individual size estimates for the 19 quasars in our sample are also in excellent agreement with the results of the joint maximum likelihood analysis.Comment: 6 pages, 3 figures, submitted to Ap

I. Flux and color variations of the quadruply imaged quasar HE 0435-1223

aims: We present VRi photometric observations of the quadruply imaged quasar HE 0435-1223, carried out with the Danish 1.54m telescope at the La Silla Observatory. Our aim was to monitor and study the magnitudes and colors of each lensed component as a function of time. methods: We monitored the object during two seasons (2008 and 2009) in the VRi spectral bands, and reduced the data with two independent techniques: difference imaging and PSF (Point Spread Function) fitting.results: Between these two seasons, our results show an evident decrease in flux by ~0.2-0.4 magnitudes of the four lensed components in the three filters. We also found a significant increase (~0.05-0.015) in their V-R and R-i color indices. conclusions: These flux and color variations are very likely caused by intrinsic variations of the quasar between the observed epochs. Microlensing effects probably also affect the brightest "A" lensed component.Comment: 10 pages, 8 figure

Further Evidence that Quasar X-Ray Emitting Regions Are Compact: X-Ray and Optical Microlensing in the Lensed Quasar Q J0158-4325

We present four new seasons of optical monitoring data and six epochs of X-ray photometry for the doubly-imaged lensed quasar Q J0158-4325. The high-amplitude, short-period microlensing variability for which this system is known has historically precluded a time delay measurement by conventional methods. We attempt to circumvent this limitation by application of a Monte Carlo microlensing analysis technique, but we are only able to prove that the delay must have the expected sign (image A leads image B). Despite our failure to robustly measure the time delay, we successfully model the microlensing at optical and X-ray wavelengths to find a half light radius for soft X-ray emission log(r_{1/2,X,soft}/cm) = 14.3^{+0.4}_{-0.5}, an upper limit on the half-light radius for hard X-ray emission log(r_{1/2,X,hard}/cm) <= 14.6 and a refined estimate of the inclination-corrected scale radius of the optical R-band (rest frame 3100 Angstrom) continuum emission region of log(r_s/cm) = 15.6+-0.3.Comment: 9 pages, 6 figures, submitted to Ap

Measuring Microlensing using Spectra of Multiply Lensed Quasars

We report on a program of spectroscopic observations of gravitationally-lensed QSOs with multiple images. We seek to establish whether microlensing is occurring in each QSO image using only single-epoch observations. We calculate flux ratios for the cores of emission lines in image pairs to set a baseline for no microlensing. The offset of the continuum flux ratios relative to this baseline yields the microlensing magnification free from extinction, as extinction affects the continuum and the lines equally. When we find chromatic microlensing, we attempt to constrain the size of the QSO accretion disk. SDSSJ1004+4112 and HE1104-1805 show chromatic microlensing with amplitudes $0.2< |\Delta m| < 0.6$ and $0.2< |\Delta m| < 0.4$ mag, respectively. Modeling the accretion disk with a Gaussian source ($I\propto \exp(-R^2/2r_s^2)$) of size $r_s\propto \lambda^p$ and using magnification maps to simulate microlensing we find $r_s(\lambda 3363)=7\pm3 light-days (18.1\pm7.8 \times 10^{15} cm$) and $p=1.1\pm 0.4$ for SDSS1004+4112, and $r_s(\lambda 3363)=6\pm2 light-days (15.5\pm5.2 \times 10^{15} cm$) and $p=0.7\pm0.1$ for HE1104-1805. For SDSSJ1029+2623 we find strong chromaticity of $\sim 0.4$ mag in the continuum flux ratio, which probably arises from microlensing although not all the available data fit within this explanation. For Q0957+561 we measure B-A magnitude differences of 0.4 mag, much greater than the $\sim$0.05 mag amplitude usually inferred from lightcurve variability. It may substantially modify the current interpretations of microlensing in this system, likely favoring the hypothesis of smaller sources and/or larger microdeflectors. For HS0818+1227, our data yield posible evidence of microlensing.Comment: 45pp, 17figs, ApJ accepted (june 4th 2012

The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

Charting the Host Adaptation of Influenza Viruses

Four influenza pandemics have struck the human population during the last 100 years causing substantial morbidity and mortality. The pandemics were caused by the introduction of a new virus into the human population from an avian or swine host or through the mixing of virus segments from an animal host with a human virus to create a new reassortant subtype virus. Understanding which changes have contributed to the adaptation of the virus to the human host is essential in assessing the pandemic potential of current and future animal viruses. Here, we develop a measure of the level of adaptation of a given virus strain to a particular host. We show that adaptation to the human host has been gradual with a timescale of decades and that none of the virus proteins have yet achieved full adaptation to the selective constraints. When the measure is applied to historical data, our results indicate that the 1918 influenza virus had undergone a period of preadaptation prior to the 1918 pandemic. Yet, ancestral reconstruction of the avian virus that founded the classical swine and 1918 human influenza lineages shows no evidence that this virus was exceptionally preadapted to humans. These results indicate that adaptation to humans occurred following the initial host shift from birds to mammals, including a significant amount prior to 1918. The 2009 pandemic virus seems to have undergone preadaptation to human-like selective constraints during its period of circulation in swine. Ancestral reconstruction along the human virus tree indicates that mutations that have increased the adaptation of the virus have occurred preferentially along the trunk of the tree. The method should be helpful in assessing the potential of current viruses to found future epidemics or pandemics

The Lick AGN Monitoring Project: Alternate Routes to a Broad-line Region Radius

It is now possible to estimate black hole masses across cosmic time, using broad emission lines in active galaxies. This technique informs our views of how galaxies and their central black holes coevolve. Unfortunately, there are many outstanding uncertainties associated with these "virial" mass estimates. One of these comes from using the accretion luminosity to infer a size for the broad-line region. Incorporating the new sample of low-luminosity active galaxies from our recent monitoring campaign at Lick Observatory, we recalibrate the radius-luminosity relation with tracers of the accretion luminosity other than the optical continuum. We find that the radius of the broad-line region scales as the square root of the X-ray and Hbeta luminosities, in agreement with recent optical studies. On the other hand, the scaling appears to be marginally steeper with narrow-line luminosities. This is consistent with a previously observed decrease in the ratio of narrow-line to X-ray luminosity with increasing total luminosity. The radius of the broad-line region correlates most tightly with Hbeta luminosity, while the X-ray and narrow-line relations both have comparable scatter of a factor of two. These correlations provide useful alternative virial BH masses in objects with no detectable optical/UV continuum emission, such as high-redshift galaxies with broad emission lines, radio-loud objects, or local active galaxies with galaxy-dominated continua.Comment: 8 pages, 1 figure, accepted for publication in Ap